Biology subjects

Bourgeois, Y.

Publications and source records attributed to Bourgeois, Y..

11 recordsLinked to original sources

bioRxiv2026

Genomic forecasting links climate-associated variation to spring phenology in the European wild apple, a crop wild relative of the cultivated apple

Climate-associated genomic variation is often used as a proxy for adaptive potential, yet whether it reflects adaptation with phenotypic consequences, rather than demography alone, is rarely tested in long-lived species. Genomic offsets forecast climate maladaptation from genotype-environment models but are seldom validated against phenotypes. We combined whole-genome resequencing, SNP and transposable element insertion polymorphism (TIP) variation, landscape genomics, genome-wide association, genomic offset, and common-garden phenotyping in the European wild apple (Malus sylvestris Mill.), a crop wild relative with a complex demographic history, to test this. Results: Of 148 resequenced accessions (135 wild, 13 cultivated), 89 wild individuals formed the core dataset. Population structure was associated with Last Glacial Maximum precipitation rather than contemporary climate, and genetic diversity increased from west to east. Genome-environment associations across 9.75 million SNPs identified climate-associated loci enriched in photoperiod-related flowering-time genes, with limited overlap with phenotype-associated loci. SNP-based genomic offset was associated with bud-break timing in the Saclay common garden (marginal R2 = 0.31), with higher offsets corresponding to earlier bud break, but not with growth or ecophysiological traits. This association depended on Austrian and Romanian populations and was clearest in non-admixed wild individuals. Offsets based on TIPs or glacial climate did not predict measured phenotypes. Conclusions: Climate association, phenotypic relevance, and predictive power of genomic variation are separable. In a long-lived tree, genomic offset predicted spring phenology, a key adaptive trait, but this signal varied across provenances and ancestries and was absent for transposable elements. Genomic offsets can therefore forecast potential phenological maladaptation, provided they are validated against phenotypes such as bud break.

ecology↗

bioRxiv2026

Reticulate evolution and climate driven diversification shaped the origin and geographic structure of Linum bienne

[vrecto] Hybridization, incomplete lineage sorting and climatic oscillations can interact across evolutionary timescales, but their combined effects on plant diversification remain difficult to resolve. We investigated how these processes shaped the origin and geographic structure of Linum bienne, the putative progenitor of cultivated flax. [vrecto]We integrated genus-level Angiosperms353 phylogenomics across Linum with plastome analyses, low-depth nuclear resequencing, demographic inference and environmental niche modelling across the range of L. bienne. This framework allowed us to assess phylogenetic discordance, test for reticulation and reconstruct lineage history through time. [vrecto]Phylogenetic discordance was widespread across our genus-level sampling and largely consistent with incomplete lineage sorting. However, branch-length and maximum-likelihood network analyses detected additional signal of gene flow at the node including L. bienne, cultivated flax and the closest relatives. Within L. bienne, plastid and nuclear data recovered four geographically structured lineages across the species range, with cytonuclear discordance and demographic analyses supporting repeated secondary contact. [vrecto]Our results show that the evolutionary history of L. bienne reflects the interaction between deep reticulation, incomplete lineage sorting and Pleistocene range dynamics. This multiscale perspective highlights L. bienne as a genetically complex species and illustrates how reticulate evolution and climatic change can jointly shape plant diversification.

evolutionary biology↗

bioRxiv2025

Contrasting genomic routes to domestication in Occidental and Oriental pears

The domestication of perennial fruit trees remains poorly understood compared with annual crops, which were shaped by strong bottlenecks and elevated genetic load. Pears (Pyrus spp.) provide an ideal model for exploring how long-lived, outcrossing crops evolved under human selection. Here, we combined high-coverage whole-genome resequencing of 396 wild and cultivated accessions from Occidental and Oriental pears with analyses of nucleotide and transposable element (TE) polymorphisms to reconstruct the demographic and adaptive history of pear domestication. Demographic inferences revealed weak or no domestication bottlenecks and extensive gene flow between wild and cultivated populations. In the Occidental lineage, dessert and perry P. communis cultivars underwent independent domestications from the same wild progenitor, P. pyraster, with divergent selection linked to fruit use. In the Oriental lineage, regionally independent domestications gave rise to Chinese and Japanese P. pyrifolia cultivars, shaped by both environmental adaptation and human selection. Selection scans identified lineage- and use-specific targets related to fruit texture, metabolism, and immunity. Contrary to the classical "cost of domestication" hypothesis, cultivated pears carried fewer deleterious variants than their wild relatives, suggesting efficient purging through selection and introgression. TE insertions mirrored population structure and occasionally occurred near selected genes, indicating a limited but detectable adaptive role. Together, our findings go beyond confirming the dual origins of Pyrus domestication to reveal contrasting demographic and adaptive pathways in Occidental and Oriental pears, illustrating independent adaptive trajectories in perennial crops, where long lifespan, self-incompatibility, and recurrent introgression shape distinctive genomic outcomes.

genomics↗

bioRxiv2025

Comprehensive annotation of olfactory and gustatory receptor genes and transposable elements revealed their evolutionary dynamics in aphids

Understanding the molecular evolution of genes involved in parasite adaptation and the role of transposable elements (TEs) in driving their diversification is key to unraveling how populations adapt to their environments. In phytophagous insects like aphids, olfactory (OR) and gustatory receptor (GR) genes are crucial for host recognition, yet their post-duplication evolution remains insufficiently explored. Here, we analyzed 521 OR and 399 GR genes, alongside TEs, across 12 aphid genomes with varying host ranges. Aphid lineages with broader host ranges exhibited higher evolutionary rates, driven by gene family expansions linked to host interaction, including lipid metabolism, immune function, and transposase activity. The evolution of OR and GR genes post-duplication was shaped by diversifying selection, with bursts of positive selection followed by long periods of purifying selection, consistent with adaptation to new hosts. OR and GR genes originated from proximal and tandem duplications, with younger TE activity enriched near these genes compared to other genomic regions, suggesting a role for TEs in catalyzing tandem duplications and fueling diversification. The star-like topology of the OR phylogenetic tree, low synteny, and recent TE activity around OR genes support a faster evolutionary rate for ORs than GRs - a trend observed in other insect taxa. This study provides insights into molecular mechanisms underlying host adaptation in aphids and presents the first high-quality genome assembly of Dysaphis plantaginea, a major apple pest, with a comprehensive annotation of chemosensory genes and TEs. These resources offer a foundation for research on aphid genome evolution, insect-plant interactions.

molecular biology↗

bioRxiv2024

Taking advantage of reference-guided assembly in a slowly-evolving lineage: application to Testudo graeca.

BackgroundObtaining de novo chromosome-level genome assemblies greatly enhances conservation and evolutionary biology studies. For many research teams, long-read sequencing technologies (that produce highly contiguous assemblies) remain unaffordable or unpractical. For the groups that display high synteny conservation, these limitations can be overcome by a reference-guided assembly using a close relative genome. Of chelonians, terrestrial tortoises are considered one of the most endangered taxa, which calls for more genomic resources. Here we make the most of high synteny conservation in chelonians to produce the first chromosome-level genome assembly of genus Testudo with one of the most iconic tortoise species in the Mediterranean basin: T. graeca. ResultsWe used high quality, paired-end Illumina sequences to build a reference-guided assembly with the chromosome level assembly of Gopherus evgoodei. We reconstructed a 2.29 Gb haploid genome with a scaffold N50 of 107.598 Mb and 5.37% gaps. We sequenced 25998 protein-coding genes, and a 41.2% fraction was determined as repetitive in our assembled genome. Demographic history reconstruction based on the genome revealed two events (population decline and recovery) consistent with previously suggested phylogeographic patterns for the species. This outlines the value of genomes like this for phylogeographic studies. ConclusionsOur results highlight the value of using close relatives to produce de novo draft assemblies in species where such resources are unavailable. Our Testudo graeca annotated genome paves the way to delve deeper into the species evolutionary history and provides a valuable resource to increase making direct conservation efforts on their threatened populations.

genomics↗

bioRxiv2021

Heat-induced transposition leads to rapid drought resistance of Arabidopsis thaliana

Eukaryotic genomes contain a vast diversity of transposable elements (TEs). Formerly often described as selfish and parasitic DNA sequences, TEs are now recognized as a source of genetic diversity and powerful drivers of evolution. Yet, because their mobility is tightly controlled by the host, studies experimentally assessing how fast TEs may mediate the emergence of adaptive traits are scare. Here, we show that the heat-induced transposition of a low-copy TE increases phenotypic diversity and leads to the emergence of drought-tolerant individuals in Arabidopsis thaliana. We exposed high-copy TE lines (hcLines) with up to [~]8 fold increased copy numbers of the heat-responsive ONSEN TE (AtCOPIA78) to drought as a straightforward and ecologically highly relevant selection pressure. We provide evidence for increased drought tolerance in five out of the 23 tested hcLines and further pinpoint one of the causative mutations to an exonic insertion of ONSEN in the ribose-5-phosphate-isomerase 2 gene. The resulting loss-of-function mutation caused a decreased rate of photosynthesis and water consumption. This is one of the rare empirical examples substantiating the adaptive potential of mobilized stress-responsive TEs in eukaryotes. Our work sheds light on the relationship between TEs and their hosts and demonstrates the importance of TE-mediated loss-of-function mutations in stress adaptation, particularly in the face of global warming.

evolutionary biology↗

bioRxiv2021

Coloring inside the lines: genomic architecture and evolution of a widespread color pattern in frogs

Traits shared among distantly related lineages are indicators of common evolutionary constraints, at the ecological, physiological or molecular level. The vertebral stripe is a color pattern that is widespread across the anuran phylogeny. Despite its prevalence in the order, surprisingly little is known about the genetic basis and evolutionary dynamic of this color pattern. Here we combine histology, genome- and transcriptome-wide analyses with order-scale phylogenetic comparative analyses to investigate this common phenotype. We show that the vertebral stripe has evolved hundreds of times in the evolutionary history of anurans and is selected for in terrestrial habitats. Using the Ethiopian Ptychadena radiation as a model system, we demonstrate that variation at the ASIP gene is responsible for the different vertebral stripe phenotypes. Alleles associated to these phenotypes are younger than the split between closely related Ptychadena species, thus indicating that the vertebral stripe results from parallel evolution within the group. Our findings demonstrate that this widespread color pattern evolves rapidly and recurrently in terrestrial anurans, and therefore constitute an ideal system to study repeated evolution.

evolutionary biology↗

bioRxiv2018

Selection at behavioral, developmental and metabolic genes is associated with the northward expansion of a successful tropical colonizer

What makes a species able to colonize novel environments? This question is key to understand the dynamics of adaptive radiations and ecological niche shifts, but the mechanisms that underlie expansion into novel habitats remain poorly understood at a genomic scale. Lizards from the genus Anolis are typically tropical and the green anole (Anolis carolinensis) constitutes an exception since it expanded into temperate North America from subtropical Florida. Thus, we used the green anole as a model to investigate signatures of selection associated with colonization of a new environment, namely temperate North America. To this end, we analyzed 29 whole genome sequences, representing the entire genetic diversity of the species. We used a combination of recent methods to quantify both positive and balancing selection in northern populations, including FST outlier methods, machine learning and ancestral recombination graphs. We naively scanned for genes of interest and assessed the overlap between multiple tests. Strikingly, we identified many genes involved in behavior, suggesting that the recent successful colonization of northern environments may have been linked to behavioral shifts as well as physiological adaptation. These results were robust to recombination, gene length and clustering. Using a candidate genes strategy, we determined that genes involved in response to cold or behavior displayed more frequently signals of selection, while controlling for local recombination rate and gene length. In addition, we found signatures of balancing selection at immune genes in all investigated genetic groups, but also at genes involved in neuronal and anatomical development in Florida.

evolutionary biology↗

bioRxiv2018

Local adaptation and sexual selection drive intra-island diversification in a songbird lineage: differential divergence in autosomes and sex chromosomes.

Recently diverged taxa showing marked phenotypic and ecological diversity are optimal systems to test the relative importance of two major evolutionary mechanisms, adaptation to local ecological conditions by natural selection, or mechanisms of reproductive isolation such as assortative mating mediated by sexually selected mating signals or post-zygotic incompatibilities. Whereas local adaptation is expected to affect many loci throughout the genome, traits acting as mating signals are expected to be located on sex chromosomes and have a simple genetic basis. We used genome-wide markers to test these predictions in Reunion Islands gray-white eye (Zosterops borbonicus), which has recently diversified into five distinct plumage forms. Two of them correspond to a polymorphic highland population that is separated by a steep ecological gradient from three distinct lowland forms that show narrow contact zones in plumage color traits, yet no association with environmental variables. An analysis of population structure using genome-wide SNP loci revealed two major clades corresponding to highland and lowland forms, respectively, with the latter separated further into three independent lineages corresponding to plumage forms. Coalescent tests of alternative demographic scenarios provided support for divergence of highland and lowland lineages with an intensification of gene flow in the last 60,000 years. Landscapes of genomic variation revealed that signatures of selection associated with elevation are found at multiple regions across the genome, whereas most loci associated with the lowland forms are located on the Z sex chromosome. A gene ontology analysis identified TYRP1, a Z-linked color gene, as a likely candidate locus underlying color variation among lowland forms. Our results are consistent with the role of natural selection in driving the divergence of locally adapted highland populations, and the role of sexual selection in differentiating lowland forms through reproductive isolation mechanisms, showing that both modes of lineage divergence can take place at very small geographic scales in birds.

evolutionary biology↗

bioRxiv2018

Recent secondary contacts, background selection and variable recombination rates shape genomic diversity in the model species Anolis carolinensis

Gaining a better understanding on how selection and neutral processes affect genomic diversity is essential to gain better insights into the mechanisms driving adaptation and speciation. However, the evolutionary processes affecting variation at a genomic scale have not been investigated in most vertebrate lineages. Previous studies have been limited to a small number of model species, mostly mammals, and no studies have investigated genomic variation in non avian reptiles. Here we present the first population genomics survey using whole genome re sequencing in the green anole (Anolis carolinensis). This species has emerged as a model for the study of genomic evolution in squamates. We quantified how demography, recombination and selection have led to the current genetic diversity of the green anole by using whole-genome resequencing of five genetic clusters covering the entire species range. The differentiation of green anoles populations is consistent with a northward expansion from South Florida followed by genetic isolation and subsequent gene flow among adjacent genetic clusters. Dispersal out-of-Florida was accompanied by a drastic population bottleneck followed by a rapid population expansion. This event was accompanied by male-biased dispersal and/or selective sweeps on the X chromosome. We show that the combined effect of background selection and recombination rates is the main contributor to the genomic landscape of differentiation in the anole genome. We further demonstrate that recombination rates are positively correlated with GC content at third codon position (GC3) and confirm the importance of biased gene conversion in shaping genome wide patterns of diversity in reptiles.

evolutionary biology↗

bioRxiv2018

Genome-wide scans of selection highlight the impact of biotic and abiotic constraints in natural populations of the model grass Brachypodium distachyon.

Grasses are essential plants for ecosystem functioning. Quantifying the selective pressures that act on natural variation in grass species is therefore essential regarding biodiversity maintenance. In this study, we investigate the selection pressures that act on two distinct populations of the grass model Brachypodium distachyon without prior knowledge about the traits under selection. We took advantage of whole-genome sequencing data produced for 44 natural accessions of B. distachyon and used complementary genome-wide scans of selection (GWSS) methods to detect genomic regions under balancing and positive selection. We show that selection is shaping genetic diversity at multiple temporal and spatial scales in this species and affects different genomic regions across the two populations. Gene Ontology annotation of candidate genes reveals that pathogens may constitute important factors of positive and balancing selection in Brachypodium distachyon. We eventually cross-validated our results with QTL data available for leaf-rust resistance in this species and demonstrate that, when paired with classical trait mapping, GWSS can help pinpointing candidate genes for further molecular validation. Thanks to a near-base perfect reference genome and the large collection of freely available natural accessions collected across its natural range, B. distachyon appears as a prime system for studies in ecology, population genomics and evolutionary biology.

evolutionary biology↗